LXL04_004648 | RubberDandelionOmics

Gene overview

LXL04_004648

Reference: OH-1004 Chr: Chr01 Coordinates: 142373431-142376685 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1878 bp · LXL04_004648|LXL04_004648|OH1004|cDNA

ATGGAGGAAGTTCAGAATGACGACAAAGATAACAATGGAAGCTCGGTGCCGGAGTCTGCTGCGGAGGAAGAGCCGATGGTGGGACCAGGCCCCGCGCCAGTCCGTCGCCCAAAGCGTCCCCTTCAATTCGAACAGGCTTATCTCGATTCCCTTCCATCTGCTAACATGTATGAAAAAAGTTACATGCATAGAGATGTGGTAACTCATGTTGCTGTTTCATCAGCTGATTTTTTCATAACAGGGAGTCAAGATGGACATTT...

CDS

Download CDS FASTA

1878 bp · LXL04_004648|LXL04_004648|OH1004|CDS

ATGGAGGAAGTTCAGAATGACGACAAAGATAACAATGGAAGCTCGGTGCCGGAGTCTGCTGCGGAGGAAGAGCCGATGGTGGGACCAGGCCCCGCGCCAGTCCGTCGCCCAAAGCGTCCCCTTCAATTCGAACAGGCTTATCTCGATTCCCTTCCATCTGCTAACATGTATGAAAAAAGTTACATGCATAGAGATGTGGTAACTCATGTTGCTGTTTCATCAGCTGATTTTTTCATAACAGGGAGTCAAGATGGACATTT...

Protein

Download Protein FASTA

625 aa · LXL04_004648|LXL04_004648|OH1004|PROTEIN

MEEVQNDDKDNNGSSVPESAAEEEPMVGPGPAPVRRPKRPLQFEQAYLDSLPSANMYEKSYMHRDVVTHVAVSSADFFITGSQDGHLKFWKKKGLGIEFAKHFRSHLGPIEGLAVSADGLLCCTISSDRSVKIYDVHNYDMMVMLRLPYTPGAVEWVYKQGAVKAKLAISDRNSSFVHIYDPRAGTNEPIISKQIHLNPVKVMKYNRALDTVVSGDTMGIIEYWDTTTLQFPENGVNFKVKSDTDLFAIVKCKTAISAIE...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_004648`
TK1151 ID	TkA01G128710
OH-1004 ID	LXL04_004648
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	91.000
Protein coverage (%)	TK1151 75.000 / OH-1004 12.480 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_004648

Location Chr01:142373431-142376685 (+)

Description Similar to CYP71: Peptidyl-prolyl cis-trans isomerase CYP71

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g44600`	PPIases accelerate the folding of proteins (Probable).	A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis.2007 · DOI: 10.1105/tpc.107.053579 Structural and functional analyses of the PPIase domain of Arabidopsis thaliana CYP71 reveal its catalytic activity toward histone H3.2021 · DOI: 10.1002/1873-3468.13965

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004648 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0009933 meristem structural organization Biological Process

GO:0010082 regulation of root meristem growth Biological Process

GO:0010305 leaf vascular tissue pattern formation Biological Process

GO:0010338 leaf formation Biological Process

GO:0010358 leaf shaping Biological Process

GO:0031507 heterochromatin formation Biological Process

GO:0045814 negative regulation of gene expression, epigenetic Biological Process

KEGG gene cross-reference

ath:AT3G44600

bta:517560

hsa:23398

mmu:238831

pon:100174766

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.563

Rank 1 · LXL04_004648 · OH-1004

Cytoplasm0.405

Rank 2 · LXL04_004648 · OH-1004

Cell membrane0.081

Rank 3 · LXL04_004648 · OH-1004

Endoplasmic reticulum0.038

Rank 4 · LXL04_004648 · OH-1004

Mitochondrion0.035

Rank 5 · LXL04_004648 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF24814.2WD40_Prp1956-225 aa

PF23381.2Beta-prop_IFT122_1st59-232 aa

PF24807.2WD40_CDC20-Fz59-144 aa

PF23409.2Beta-prop_EML59-160 aa

PF25047.1Beta-prop_TEP1_2nd60-229 aa

PF25172.2Beta-prop_WDR3_2nd61-135 aa

PF25175.2Beta-prop_WDR562-231 aa

PF25173.2Beta-prop_WDR3_1st62-136 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004648	`PF24814.2`	WD40_Prp19	56	225	1.5e-11	44.6
LXL04_004648	`PF23381.2`	Beta-prop_IFT122_1st	59	232	2.4e-11	44.2
LXL04_004648	`PF24807.2`	WD40_CDC20-Fz	59	144	4.6e-10	40.0
LXL04_004648	`PF23409.2`	Beta-prop_EML	59	160	1.3e-08	35.4
LXL04_004648	`PF25047.1`	Beta-prop_TEP1_2nd	60	229	1.3e-08	35.1
LXL04_004648	`PF25172.2`	Beta-prop_WDR3_2nd	61	135	9.7e-10	38.8
LXL04_004648	`PF25175.2`	Beta-prop_WDR5	62	231	6.1e-18	65.8
LXL04_004648	`PF25173.2`	Beta-prop_WDR3_1st	62	136	1.8e-12	48.1
LXL04_004648	`PF25174.2`	Beta-prop_THOC3	63	294	9.4e-15	55.1
LXL04_004648	`PF24805.2`	EIF3I	75	291	2.1e-07	31.1
LXL04_004648	`PF24796.2`	WDR55	102	228	6.7e-11	42.5
LXL04_004648	`PF00160.27`	Pro_isomerase	472	622	4e-57	193.6

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q8W4D0`	Arabidopsis thaliana	Peptidyl-prolyl cis-trans isomerase CYP71	85.833%	Swiss-Prot	strong database homology

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